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- PDB-6szh: Acinetobacter baumannii undecaprenyl pyrophosphate synthase (AB-U... -

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Basic information

Entry
Database: PDB / ID: 6szh
TitleAcinetobacter baumannii undecaprenyl pyrophosphate synthase (AB-UppS) in complex with GW197
ComponentsDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
KeywordsTRANSFERASE / Inhibitor Complex
Function / homology
Function and homology information


ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / magnesium ion binding / cytosol
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,5-dimethyl-1~{H}-pyrrole-2-carbonitrile / Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsThorpe, J.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Cocktailed fragment screening by X-ray crystallography of the antibacterial target undecaprenyl pyrophosphate synthase from Acinetobacter baumannii.
Authors: Thorpe, J.H. / Wall, I.D. / Sinnamon, R.H. / Taylor, A.N. / Stavenger, R.A.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
B: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9704
Polymers61,8102
Non-polymers1602
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-35 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.300, 64.120, 71.600
Angle α, β, γ (deg.)90.000, 92.700, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-487-

HOH

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Components

#1: Protein Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) / Ditrans / polycis-undecaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS / ...Ditrans / polycis-undecaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS / Undecaprenyl pyrophosphate synthase / UPP synthase


Mass: 30904.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ispU, uppS, uppS_2, A7M79_11260, A7M90_02080, A7N09_13955, AB719_02530, B4R90_04635, B9X91_17010, B9X95_06890, BWP00_01470, CBE85_15965, CEJ63_18040, CSB70_2045, CYQ93_09555, D3X57_15480, DCD77_ ...Gene: ispU, uppS, uppS_2, A7M79_11260, A7M90_02080, A7N09_13955, AB719_02530, B4R90_04635, B9X91_17010, B9X95_06890, BWP00_01470, CBE85_15965, CEJ63_18040, CSB70_2045, CYQ93_09555, D3X57_15480, DCD77_00905, DOL94_09555, DVA79_11950, E2535_15455, E4664_05920, EA685_17420, EA722_15190, EHF38_07755, EJB02_03910, EWO92_00565, EWO96_03250, EWP49_03250, FDF20_10270, LV38_00732, NCTC13305_00281, SAMEA104305177_04421, SAMEA104305229_03969, SAMEA104305268_02140, SAMEA104305283_01949, SAMEA104305292_00210, SAMEA104305315_07345, SAMEA104305318_03206, SAMEA104305320_02219, SAMEA104305325_00455, SAMEA104305337_07638
Production host: Escherichia coli K-12 (bacteria)
References: UniProt: V5VCK8, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-M2H / 3,5-dimethyl-1~{H}-pyrrole-2-carbonitrile


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200mM Calcium Acetate, 20% PEG 3350 and 20% Glycerol (+ crystal seeds)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.647→71.521 Å / Num. obs: 52406 / % possible obs: 85.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 26.81 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.033 / Net I/σ(I): 21.6
Reflection shellResolution: 1.647→1.736 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2618 / CC1/2: 0.776 / Rrim(I) all: 0.582 / % possible all: 32.4

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X07

1x07


Resolution: 1.65→23.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2625 5.01 %RANDOM
Rwork0.183 ---
obs0.185 52398 79.5 %-
Displacement parametersBiso max: 142.43 Å2 / Biso mean: 31.32 Å2 / Biso min: 11.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.1186 Å20 Å2-0.065 Å2
2---0.3361 Å20 Å2
3---0.4546 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.65→23.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 10 324 3870
Biso mean--30.15 38.92 -
Num. residues----439
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1303SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes652HARMONIC5
X-RAY DIFFRACTIONt_it3684HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion474SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4494SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3684HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5012HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion15.15
LS refinement shellResolution: 1.65→1.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.242 37 3.53 %
Rwork0.2197 1011 -
all0.2204 1048 -
obs--30.66 %

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